NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P30365 UniProt NPD GO	NO12_MEDTR	Early nodulin 12 precursor (N-12)	0.19	-	nuc	1 *	Cell wall (Potential)				103
Q754C8 UniProt NPD GO	EF2_ASHGO	Elongation factor 2 (EF-2)	0.19	-	cyt	0	Cytoplasm (By similarity)				842
Q5R9V1 UniProt NPD GO	EFG1_PONPY	Elongation factor G 1, mitochondrial precursor (mEF-G 1) (Elongation factor G1)	0.19	-	nuc	0	Mitochondrion				751
P25039 UniProt NPD GO	EFG1_YEAST	Elongation factor G 1, mitochondrial precursor (mEF-G-1) (EFGM)	0.19	-	nuc	0	Mitochondrion	mitochondrion [IDA]			761
P40319 UniProt NPD GO	ELO3_YEAST	Elongation of fatty acids protein 3 (SUR4 protein) (SRE1 protein) (v-SNARE bypass mutant gene 1 prot ...	0.19	-	end	6	Membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum [IDA] endoplasmic reticulum membrane [TAS]			345
P07982 UniProt NPD GO	GUN2_TRIRE	Endoglucanase EG-II precursor (EC 3.2.1.4) (Endo-1,4-beta-glucanase) (Cellulase) (EGLII)	0.19	-	nuc	0					418
Q6FRZ3 UniProt NPD GO	ERV25_CANGA	Endoplasmic reticulum vesicle protein 25 precursor	0.19	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				208
Q9AXH9 UniProt NPD GO	KAO1_HORVU	Ent-kaurenoic acid oxidase 1 (EC 1.14.13.79) (gpr5)	0.19	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				499
Q8MIT7 UniProt NPD GO	CCL11_MACMU	Eotaxin precursor (Small inducible cytokine A11) (CCL11)	0.19	-	exc	0	Secreted protein				97
O13146 UniProt NPD GO	EPHA3_BRARE	Ephrin type-A receptor 3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor ZEK1) (EPH-like k ...	0.19	-	nuc	1	Membrane; single-pass type I membrane protein				981
Q07498 UniProt NPD GO	EPHB3_CHICK	Ephrin type-B receptor 3 (EC 2.7.10.1) (Tyrosine-protein kinase receptor CEK10) (Fragment)	0.19	-	nuc	1	Membrane; single-pass type I membrane protein				988
Q9BDL1 UniProt NPD GO	EPPI_MACMU	Eppin precursor (Epididymal protease inhibitor) (Serine protease inhibitor-like with Kunitz and WAP ...	0.19	-	exc	0	Secreted protein (Potential)				133
P12962 UniProt NPD GO	IF43_YEAST	Eukaryotic initiation factor 4F subunit p20 (eIF-4F) (20 kDa cap-associated protein)	0.19	-	cyt	0		mRNA cap complex [IPI]			177
Q5CD84 UniProt NPD GO	ERF1_LOXST	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.19	-	cyt	0	Cytoplasm (By similarity)				436
P56331 UniProt NPD GO	IF1A_ONOVI	Eukaryotic translation initiation factor 1A (EIF-1A) (EIF-4C)	0.19	-	nuc	0					144
P29338 UniProt NPD GO	IF4E_RABIT	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.19	-	cyt	0					217
P62695 UniProt NPD GO	GUX1_TRIKO	Exoglucanase 1 precursor (EC 3.2.1.91) (Exoglucanase I) (Exocellobiohydrolase I) (CBHI) (1,4-beta-ce ...	0.19	-	exc	0	Secreted protein				513
P62694 UniProt NPD GO	GUX1_TRIRE	Exoglucanase 1 precursor (EC 3.2.1.91) (Exoglucanase I) (Exocellobiohydrolase I) (CBHI) (1,4-beta-ce ...	0.19	-	exc	0	Secreted protein			8CEL	513
Q9M1G9 UniProt NPD GO	EXTN2_ARATH	Extensin-2 precursor (AtExt2) (Cell wall hydroxyproline-rich glycoprotein 1) (HRGP1)	0.19	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				743
Q2QLG4 UniProt NPD GO	CAZA2_CALJA	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.19	-	nuc	0					285
P38352 UniProt NPD GO	YB9W_YEAST	F-box protein YBR280C	0.19	-	nuc	0					637
Q95L05 UniProt NPD GO	FKBP5_CERAE	FK506-binding protein 5 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (51 kDa FK506-binding imm ...	0.19	-	cyt	0	Cytoplasm (By similarity)				457
Q13451 UniProt NPD GO	FKBP5_HUMAN	FK506-binding protein 5 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (51 k ...	0.19	-	cyt	0	Cytoplasm. Nucleus		602623	1KT0	457
Q9PT41 UniProt NPD GO	VSP1_VIPLE	Factor V-activating enzyme precursor (EC 3.4.21.-) (FVA)	0.19	-	exc	0	Secreted protein				259
P70623 UniProt NPD GO	FABPA_RAT	Fatty acid-binding protein, adipocyte (AFABP) (Adipocyte lipid-binding protein) (ALBP) (A-FABP)	0.19	-	cyt	0	Cytoplasm (Potential)				131
Q04800 UniProt NPD GO	FRP1_SCHPO	Ferric reductase transmembrane component (EC 1.16.1.7) (Ferric-chelate reductase)	0.19	-	end	6 *	Membrane; multi-pass membrane protein				564
P19130 UniProt NPD GO	FRIH_PIG	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.19	-	nuc	0					180
P09451 UniProt NPD GO	FRIL_RABIT	Ferritin light chain (Ferritin L subunit)	0.19	-	cyt	0					174
Q7SXA5 UniProt NPD GO	FRIL_XENLA	Ferritin light chain, oocyte isoform (B-ferritin) (XeBF) (GV-LCH)	0.19	-	cyt	0					177
P07798 UniProt NPD GO	FRI2_RANCA	Ferritin, middle subunit (EC 1.16.3.1) (Ferritin M) (Ferritin X) (Ferritin H')	0.19	-	cyt	0				1MFR	175
Q8I1F4 UniProt NPD GO	FBRL_DROER	Fibrillarin	0.19	+	cyt	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)	dense fibrillar component [ISS]			345
Q9W1V3 UniProt NPD GO	FBRL_DROME	Fibrillarin	0.19	+	cyt	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)	dense fibrillar component [ISS]			344
P04115 UniProt NPD GO	FIBG_PETMA	Fibrinogen gamma chain precursor	0.19	-	exc	0	Secreted protein			1N73	432
P12799 UniProt NPD GO	FIBG_BOVIN	Fibrinogen gamma-B chain precursor (Gamma')	0.19	-	vac	0	Secreted protein			1JY3	444
P52838 UniProt NPD GO	FSTL_FLABI	Flavonol sulfotransferase-like (EC 2.8.2.-)	0.19	-	cyt	0	Cytoplasm (Potential)				309
Q14254 UniProt NPD GO	FLOT2_HUMAN	Flotillin-2 (Epidermal surface antigen) (ESA)	0.19	-	cyt	0	Cell membrane; caveola; peripheral membrane protein. Membrane-associated protein of caveolae	cell surface [IEP] plasma membrane [NAS]	131560		379
Q8R428 UniProt NPD GO	FSHR_CAVPO	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.19	-	end	7	Membrane; multi-pass membrane protein				695
P35378 UniProt NPD GO	FSHR_MOUSE	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.19	+	end	7	Membrane; multi-pass membrane protein				692
P49059 UniProt NPD GO	FSHR_PIG	Follicle-stimulating hormone receptor precursor (FSH-R) (Follitropin receptor)	0.19	-	end	7	Membrane; multi-pass membrane protein				695
Q8NFU4 UniProt NPD GO	FDSCP_HUMAN	Follicular dendritic cell secreted peptide precursor (FDC-SP) (FDC secreted protein)	0.19	-	exc	1 *	Secreted protein		607241		85
Q9UP38 UniProt NPD GO	FZD1_HUMAN	Frizzled-1 precursor (Fz-1) (hFz1) (FzE1)	0.19	-	end	7	Membrane; multi-pass membrane protein		603408		647
P00637 UniProt NPD GO	F16P1_RABIT	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase 1) (FBPa ...	0.19	-	cyt	0				1BK4	337
Q64362 UniProt NPD GO	FTS1_MOUSE	Fused toes protein (FT1)	0.19	-	cyt	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity)				292
P48548 UniProt NPD GO	IRK5_RAT	G protein-activated inward rectifier potassium channel 4 (GIRK4) (Potassium channel, inwardly rectif ...	0.19	-	end	2	Membrane; multi-pass membrane protein				419
Q8K3J9 UniProt NPD GO	GPC5C_MOUSE	G-protein coupled receptor family C group 5 member C precursor (Retinoic acid-induced gene 3 protein ...	0.19	-	end	8 *	Membrane; multi-pass membrane protein	mitochondrion [IDA]			440
Q70VB1 UniProt NPD GO	GPC6A_RAT	G-protein coupled receptor family C group 6 member A precursor	0.19	-	end	7	Cell membrane; multi-pass membrane protein				928
P93411 UniProt NPD GO	CCNC_ORYSA	G1/S-specific cyclin C-type	0.19	-	mit	0					257
Q6BWE3 UniProt NPD GO	MCD4_DEBHA	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.19	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				990
P38548 UniProt NPD GO	RAN_VICFA	GTP-binding nuclear protein Ran/TC4	0.19	-	cyt	0	Nucleus (By similarity)				221
P54765 UniProt NPD GO	RAN1A_LOTJA	GTP-binding nuclear protein Ran1A (Fragment)	0.19	-	cyt	0	Nucleus (By similarity)				209

You are viewing entries 51801 to 51850 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.